Starting phenix.real_space_refine on Mon May 26 01:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.map" model { file = "/net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z83_39837/05_2025/8z83_39837.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 58 5.49 5 Mg 46 5.21 5 S 100 5.16 5 C 19326 2.51 5 N 3784 2.21 5 O 4679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27998 Number of models: 1 Model: "" Number of chains: 74 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2618 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 314} Chain: "L" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2170 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "M" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2518 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain: "H" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2174 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 253} Chain: "A" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "F" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "I" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "K" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Q" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "T" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "U" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "W" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "4" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "5" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "6" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "7" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "8" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "9" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "0" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 283 Unusual residues: {' MG': 1, 'HEC': 4, 'LMT': 1, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 569 Unusual residues: {'BCL': 3, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'UQ8:plan-4': 1, 'UQ8:plan-6': 3, 'UQ8:plan-7': 3, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-8': 3, 'UQ8:plan-9': 2} Unresolved non-hydrogen planarities: 74 Chain: "M" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 543 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 5, 'CRT': 1, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 186 Chain: "H" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 260 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 163 Unusual residues: {'BCL': 1, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "N" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 161 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "P" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "V" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'PGV:plan-3': 2, 'PGV:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'PGV:plan-1': 2} Unresolved non-hydrogen planarities: 10 Chain: "1" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2, 'PGV:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'PGV:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "5" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "8" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 16 Chain: "9" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 17.81, per 1000 atoms: 0.64 Number of scatterers: 27998 At special positions: 0 Unit cell: (129.56, 132.84, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 100 16.00 P 58 15.00 Mg 46 11.99 O 4679 8.00 N 3784 7.00 C 19326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=59, symmetry=0 Number of additional bonds: simple=59, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.13 Conformation dependent library (CDL) restraints added in 2.8 seconds 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4942 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 11 sheets defined 64.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.550A pdb=" N ILE C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.395A pdb=" N THR C 109 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 152 through 158 removed outlier: 3.787A pdb=" N CYS C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.659A pdb=" N THR C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.114A pdb=" N CYS C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.960A pdb=" N LEU C 261 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 288 removed outlier: 4.103A pdb=" N GLU C 272 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 32 through 58 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.612A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 220 removed outlier: 3.540A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 250 removed outlier: 3.581A pdb=" N GLY L 228 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.664A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 269 through 273 removed outlier: 3.978A pdb=" N SER L 273 " --> pdb=" O PRO L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.880A pdb=" N ILE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.596A pdb=" N LYS M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.601A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 112 through 117 Processing helix chain 'H' and resid 118 through 122 Processing helix chain 'H' and resid 154 through 161 Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 235 through 241 Processing helix chain 'H' and resid 251 through 269 removed outlier: 3.574A pdb=" N GLY H 265 " --> pdb=" O TYR H 261 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL H 266 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU H 267 " --> pdb=" O GLY H 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 9 through 35 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.808A pdb=" N ILE D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 35 Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.529A pdb=" N ALA E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 9 through 35 Processing helix chain 'G' and resid 11 through 44 Processing helix chain 'I' and resid 3 through 8 removed outlier: 3.569A pdb=" N ILE I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.500A pdb=" N VAL I 15 " --> pdb=" O ARG I 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 9 through 35 Processing helix chain 'N' and resid 11 through 44 Processing helix chain 'O' and resid 1 through 7 removed outlier: 3.825A pdb=" N MET O 4 " --> pdb=" O MET O 1 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP O 5 " --> pdb=" O TRP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 34 removed outlier: 3.692A pdb=" N VAL O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 3 through 8 Processing helix chain 'Q' and resid 9 through 35 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 2 through 7 removed outlier: 3.510A pdb=" N TRP S 5 " --> pdb=" O TRP S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 34 removed outlier: 3.651A pdb=" N VAL S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'V' and resid 11 through 44 Processing helix chain 'W' and resid 1 through 7 removed outlier: 3.661A pdb=" N MET W 4 " --> pdb=" O MET W 1 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP W 5 " --> pdb=" O TRP W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 35 Processing helix chain 'X' and resid 11 through 44 Processing helix chain 'Y' and resid 3 through 8 Processing helix chain 'Y' and resid 9 through 35 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.682A pdb=" N LYS Z 16 " --> pdb=" O ASP Z 12 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 7 Processing helix chain '1' and resid 9 through 35 removed outlier: 3.565A pdb=" N VAL 1 15 " --> pdb=" O ARG 1 11 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 44 Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 9 through 35 Processing helix chain '4' and resid 11 through 44 Processing helix chain '5' and resid 3 through 8 removed outlier: 3.811A pdb=" N ILE 5 7 " --> pdb=" O ARG 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 35 Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 1 through 7 Processing helix chain '7' and resid 9 through 35 Processing helix chain '8' and resid 11 through 44 removed outlier: 3.537A pdb=" N MET 8 23 " --> pdb=" O HIS 8 19 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 8 removed outlier: 3.759A pdb=" N ILE 9 7 " --> pdb=" O ARG 9 3 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 35 Processing helix chain '0' and resid 11 through 44 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 167 Processing sheet with id=AA3, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA7, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AA8, first strand: chain 'H' and resid 68 through 71 Processing sheet with id=AA9, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AB1, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.470A pdb=" N ILE H 184 " --> pdb=" O MET H 201 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET H 201 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP H 186 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU H 199 " --> pdb=" O ASP H 186 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 188 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG H 195 " --> pdb=" O ASP H 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.759A pdb=" N GLY H 182 " --> pdb=" O VAL H 173 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9667 1.38 - 1.56: 18901 1.56 - 1.74: 116 1.74 - 1.92: 189 1.92 - 2.11: 192 Bond restraints: 29065 Sorted by residual: bond pdb=" CA7 CDL M 402 " pdb=" OA8 CDL M 402 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CB7 CDL M 402 " pdb=" OB8 CDL M 402 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL M 410 " pdb=" OB8 CDL M 410 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL F 101 " pdb=" OB8 CDL F 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL U 101 " pdb=" OB8 CDL U 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 29060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 37982 4.91 - 9.82: 1709 9.82 - 14.73: 124 14.73 - 19.64: 36 19.64 - 24.56: 11 Bond angle restraints: 39862 Sorted by residual: angle pdb=" C2 CRT R 101 " pdb=" C1 CRT R 101 " pdb=" C4 CRT R 101 " ideal model delta sigma weight residual 110.24 85.68 24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C2 CRT Z 102 " pdb=" C1 CRT Z 102 " pdb=" C4 CRT Z 102 " ideal model delta sigma weight residual 110.24 85.69 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C2 CRT N 102 " pdb=" C1 CRT N 102 " pdb=" C4 CRT N 102 " ideal model delta sigma weight residual 110.24 85.94 24.30 3.00e+00 1.11e-01 6.56e+01 angle pdb=" C2 CRT 4 101 " pdb=" C1 CRT 4 101 " pdb=" C4 CRT 4 101 " ideal model delta sigma weight residual 110.24 85.95 24.29 3.00e+00 1.11e-01 6.55e+01 angle pdb=" C2 CRT V 102 " pdb=" C1 CRT V 102 " pdb=" C4 CRT V 102 " ideal model delta sigma weight residual 110.24 86.48 23.76 3.00e+00 1.11e-01 6.27e+01 ... (remaining 39857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 15273 35.30 - 70.61: 1039 70.61 - 105.91: 159 105.91 - 141.21: 73 141.21 - 176.52: 13 Dihedral angle restraints: 16557 sinusoidal: 8890 harmonic: 7667 Sorted by residual: dihedral pdb=" C1 BCL Z 103 " pdb=" CGA BCL Z 103 " pdb=" O2A BCL Z 103 " pdb=" CBA BCL Z 103 " ideal model delta sinusoidal sigma weight residual -180.00 -40.89 -139.11 1 6.00e+00 2.78e-02 4.68e+02 dihedral pdb=" C1 BCL I 102 " pdb=" CGA BCL I 102 " pdb=" O2A BCL I 102 " pdb=" CBA BCL I 102 " ideal model delta sinusoidal sigma weight residual 180.00 94.24 85.76 1 6.00e+00 2.78e-02 2.47e+02 dihedral pdb=" C1 BCL 3 102 " pdb=" CGA BCL 3 102 " pdb=" O2A BCL 3 102 " pdb=" CBA BCL 3 102 " ideal model delta sinusoidal sigma weight residual -180.00 -108.62 -71.38 1 6.00e+00 2.78e-02 1.82e+02 ... (remaining 16554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3095 0.058 - 0.116: 530 0.116 - 0.174: 152 0.174 - 0.233: 38 0.233 - 0.291: 33 Chirality restraints: 3848 Sorted by residual: chirality pdb=" C05 PGV E 102 " pdb=" C04 PGV E 102 " pdb=" C06 PGV E 102 " pdb=" O05 PGV E 102 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C05 PGV 1 101 " pdb=" C04 PGV 1 101 " pdb=" C06 PGV 1 101 " pdb=" O05 PGV 1 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C05 PGV Z 101 " pdb=" C04 PGV Z 101 " pdb=" C06 PGV Z 101 " pdb=" O05 PGV Z 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3845 not shown) Planarity restraints: 4636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL I 102 " -0.371 3.00e-02 1.11e+03 3.08e-01 5.26e+02 pdb=" CBA BCL I 102 " -0.119 3.00e-02 1.11e+03 pdb=" CGA BCL I 102 " 0.076 3.00e-02 1.11e+03 pdb=" O1A BCL I 102 " -0.133 3.00e-02 1.11e+03 pdb=" O2A BCL I 102 " 0.547 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 3 102 " -0.377 3.00e-02 1.11e+03 3.06e-01 5.21e+02 pdb=" CBA BCL 3 102 " -0.177 3.00e-02 1.11e+03 pdb=" CGA BCL 3 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL 3 102 " -0.065 3.00e-02 1.11e+03 pdb=" O2A BCL 3 102 " 0.533 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 101 " -0.330 3.00e-02 1.11e+03 2.66e-01 3.92e+02 pdb=" CBA BCL T 101 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL T 101 " 0.078 3.00e-02 1.11e+03 pdb=" O1A BCL T 101 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL T 101 " 0.447 3.00e-02 1.11e+03 ... (remaining 4633 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 125 2.44 - 3.06: 16453 3.06 - 3.67: 44695 3.67 - 4.29: 75255 4.29 - 4.90: 119393 Nonbonded interactions: 255921 Sorted by model distance: nonbonded pdb="MG MG C 405 " pdb=" O HOH C 502 " model vdw 1.828 2.170 nonbonded pdb="MG MG C 405 " pdb=" O HOH M 501 " model vdw 1.981 2.170 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.000 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.057 2.260 nonbonded pdb="MG MG C 405 " pdb=" O HOH C 501 " model vdw 2.094 2.170 ... (remaining 255916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 9 through 53) selection = (chain '2' and resid 9 through 53) selection = (chain '6' and resid 9 through 53) selection = (chain 'E' and resid 9 through 53) selection = (chain 'J' and resid 9 through 53) selection = (chain 'P' and resid 9 through 53) selection = (chain 'T' and resid 9 through 53) selection = (chain 'X' and resid 9 through 53) } ncs_group { reference = (chain '1' and (resid 1 through 46 or resid 102)) selection = (chain '5' and (resid 1 through 46 or resid 102)) selection = (chain '9' and (resid 1 through 46 or resid 102)) selection = (chain 'D' and (resid 1 through 46 or resid 102)) selection = (chain 'I' and (resid 1 through 46 or resid 102)) selection = (chain 'O' and (resid 1 through 46 or resid 102)) selection = (chain 'S' and (resid 1 through 46 or resid 102)) selection = (chain 'W' and (resid 1 through 46 or resid 102)) } ncs_group { reference = (chain '3' and resid 1 through 46) selection = (chain '7' and resid 1 through 46) selection = (chain 'A' and resid 1 through 46) selection = (chain 'F' and resid 1 through 46) selection = (chain 'K' and resid 1 through 46) selection = (chain 'Q' and resid 1 through 46) selection = (chain 'U' and resid 1 through 46) selection = (chain 'Y' and resid 1 through 46) } ncs_group { reference = (chain '4' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain '8' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'B' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C29 or name O0 \ 1 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or nam \ e O14 or name P )))) selection = (chain 'G' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'N' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'R' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C14 or name C2 or name C20 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )))) selection = (chain 'V' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'Z' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 59.130 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.571 29124 Z= 1.173 Angle : 2.019 24.556 39862 Z= 0.864 Chirality : 0.058 0.291 3848 Planarity : 0.022 0.308 4636 Dihedral : 23.546 176.516 11615 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.32 % Allowed : 5.41 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.16), residues: 2605 helix: 1.98 (0.12), residues: 1471 sheet: 0.68 (0.70), residues: 54 loop : 0.11 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 5 HIS 0.006 0.001 HIS W 29 PHE 0.025 0.001 PHE C 345 TYR 0.021 0.001 TYR L 164 ARG 0.003 0.000 ARG M 136 Details of bonding type rmsd hydrogen bonds : bond 0.17718 ( 1338) hydrogen bonds : angle 5.97231 ( 3837) covalent geometry : bond 0.02098 (29065) covalent geometry : angle 2.01924 (39862) Misc. bond : bond 0.18183 ( 59) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 2.603 Fit side-chains REVERT: C 131 MET cc_start: 0.9111 (mmt) cc_final: 0.8385 (mmt) REVERT: C 328 MET cc_start: 0.7721 (ptt) cc_final: 0.7322 (ptm) REVERT: H 221 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7355 (ttp-110) REVERT: E 29 TYR cc_start: 0.8816 (t80) cc_final: 0.8475 (t80) REVERT: V 13 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6154 (mm-30) REVERT: V 23 MET cc_start: 0.8332 (mmm) cc_final: 0.8107 (mmm) REVERT: Z 27 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (tp) REVERT: 3 1 MET cc_start: 0.6725 (tpp) cc_final: 0.6348 (tpp) REVERT: 4 13 GLU cc_start: 0.6707 (pp20) cc_final: 0.6434 (pp20) REVERT: 5 12 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7074 (ttt-90) REVERT: 7 9 ASP cc_start: 0.7522 (t0) cc_final: 0.7205 (t0) outliers start: 51 outliers final: 27 residues processed: 403 average time/residue: 1.5425 time to fit residues: 712.7325 Evaluate side-chains 342 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 221 ARG Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain S residue 4 MET Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 HIS L 264 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN B 24 GLN G 24 GLN O 42 GLN W 44 ASN 4 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102789 restraints weight = 36164.229| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.27 r_work: 0.3088 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.380 29124 Z= 0.217 Angle : 0.852 16.258 39862 Z= 0.330 Chirality : 0.044 0.309 3848 Planarity : 0.005 0.073 4636 Dihedral : 23.654 174.556 6951 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.68 % Allowed : 9.04 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2605 helix: 2.08 (0.12), residues: 1470 sheet: 0.50 (0.65), residues: 64 loop : -0.22 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 252 HIS 0.009 0.002 HIS W 29 PHE 0.025 0.002 PHE C 345 TYR 0.023 0.002 TYR L 164 ARG 0.009 0.001 ARG S 12 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 1338) hydrogen bonds : angle 4.50823 ( 3837) covalent geometry : bond 0.00517 (29065) covalent geometry : angle 0.85221 (39862) Misc. bond : bond 0.08345 ( 59) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 319 time to evaluate : 2.656 Fit side-chains REVERT: C 96 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: H 16 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7638 (mpm) REVERT: H 254 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: I 6 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8066 (mttt) REVERT: J 17 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: P 17 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7434 (mt-10) REVERT: R 51 GLU cc_start: 0.8293 (pm20) cc_final: 0.8027 (pm20) REVERT: T 14 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6795 (mt-10) REVERT: V 13 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: V 23 MET cc_start: 0.8459 (mmm) cc_final: 0.8173 (mmm) REVERT: Z 11 SER cc_start: 0.7207 (p) cc_final: 0.6934 (p) REVERT: Z 17 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: Z 27 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8331 (tp) REVERT: 3 1 MET cc_start: 0.6793 (tpp) cc_final: 0.6361 (tpp) REVERT: 4 13 GLU cc_start: 0.6786 (pp20) cc_final: 0.6482 (pp20) REVERT: 5 12 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.6886 (ttm110) REVERT: 5 36 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7765 (tp30) outliers start: 81 outliers final: 40 residues processed: 369 average time/residue: 1.5131 time to fit residues: 644.3801 Evaluate side-chains 345 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain 1 residue 9 ASP Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 18 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 226 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 138 GLN H 172 GLN B 24 GLN D 18 HIS G 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 44 ASN 8 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105341 restraints weight = 36253.376| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.35 r_work: 0.3119 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.306 29124 Z= 0.204 Angle : 0.726 14.809 39862 Z= 0.279 Chirality : 0.040 0.385 3848 Planarity : 0.004 0.072 4636 Dihedral : 20.994 164.477 6940 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.36 % Allowed : 10.13 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.16), residues: 2605 helix: 2.35 (0.12), residues: 1470 sheet: 0.61 (0.75), residues: 44 loop : -0.18 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.006 0.001 HIS W 29 PHE 0.019 0.001 PHE C 345 TYR 0.018 0.001 TYR L 164 ARG 0.007 0.000 ARG W 12 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 1338) hydrogen bonds : angle 4.26403 ( 3837) covalent geometry : bond 0.00332 (29065) covalent geometry : angle 0.72629 (39862) Misc. bond : bond 0.07291 ( 59) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 2.773 Fit side-chains REVERT: C 95 MET cc_start: 0.8720 (mmt) cc_final: 0.7606 (mmt) REVERT: C 164 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: H 254 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: E 29 TYR cc_start: 0.8824 (t80) cc_final: 0.8362 (t80) REVERT: J 9 ASN cc_start: 0.4742 (t0) cc_final: 0.4174 (t0) REVERT: N 51 GLU cc_start: 0.7549 (pm20) cc_final: 0.7348 (pm20) REVERT: O 42 GLN cc_start: 0.8330 (tt0) cc_final: 0.7920 (tp40) REVERT: P 17 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7435 (mt-10) REVERT: T 14 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6620 (mt-10) REVERT: V 13 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6345 (mm-30) REVERT: V 23 MET cc_start: 0.8445 (mmm) cc_final: 0.8173 (mmm) REVERT: Y 3 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7542 (mtt90) REVERT: Z 11 SER cc_start: 0.7077 (p) cc_final: 0.6791 (p) REVERT: Z 14 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7120 (mt-10) REVERT: Z 17 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: 3 1 MET cc_start: 0.6741 (tpp) cc_final: 0.6300 (tpp) REVERT: 4 13 GLU cc_start: 0.6809 (pp20) cc_final: 0.6599 (pp20) REVERT: 5 12 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.6886 (ttm110) REVERT: 6 51 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: 7 9 ASP cc_start: 0.7295 (t0) cc_final: 0.7059 (t0) REVERT: 8 27 LEU cc_start: 0.8245 (tp) cc_final: 0.7826 (tt) REVERT: 8 51 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7378 (mm-30) outliers start: 74 outliers final: 32 residues processed: 374 average time/residue: 1.5230 time to fit residues: 660.7589 Evaluate side-chains 340 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 6 residue 51 GLU Chi-restraints excluded: chain 7 residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 51 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104708 restraints weight = 36491.528| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.32 r_work: 0.3111 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 29124 Z= 0.153 Angle : 0.732 14.457 39862 Z= 0.282 Chirality : 0.040 0.376 3848 Planarity : 0.004 0.071 4636 Dihedral : 20.148 152.440 6926 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.63 % Allowed : 10.31 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2605 helix: 2.36 (0.12), residues: 1476 sheet: 0.35 (0.68), residues: 54 loop : -0.18 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 PHE 0.020 0.001 PHE H 21 TYR 0.020 0.001 TYR L 164 ARG 0.007 0.000 ARG W 12 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 1338) hydrogen bonds : angle 4.20530 ( 3837) covalent geometry : bond 0.00357 (29065) covalent geometry : angle 0.73172 (39862) Misc. bond : bond 0.05999 ( 59) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 316 time to evaluate : 2.882 Fit side-chains REVERT: C 95 MET cc_start: 0.8724 (mmt) cc_final: 0.7529 (mmt) REVERT: C 96 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: C 131 MET cc_start: 0.8976 (mmt) cc_final: 0.8396 (mmt) REVERT: C 309 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8431 (mtpt) REVERT: L 8 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8234 (tptt) REVERT: M 216 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8424 (t80) REVERT: H 254 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: I 1 MET cc_start: 0.6828 (mmt) cc_final: 0.6461 (mmt) REVERT: P 17 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7429 (mt-10) REVERT: Q 6 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7843 (mmmm) REVERT: T 14 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6600 (mt-10) REVERT: T 16 LYS cc_start: 0.8193 (mptt) cc_final: 0.7646 (mtpt) REVERT: V 13 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6313 (mm-30) REVERT: V 23 MET cc_start: 0.8428 (mmm) cc_final: 0.8125 (mmm) REVERT: W 12 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7618 (ttm-80) REVERT: Y 3 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7568 (mtt90) REVERT: Z 11 SER cc_start: 0.7114 (p) cc_final: 0.6786 (p) REVERT: Z 14 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7152 (mt-10) REVERT: Z 17 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: 3 1 MET cc_start: 0.6751 (tpp) cc_final: 0.6309 (tpp) REVERT: 4 13 GLU cc_start: 0.6833 (pp20) cc_final: 0.6516 (pp20) REVERT: 5 12 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6936 (ttt-90) REVERT: 5 36 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: 8 27 LEU cc_start: 0.8261 (tp) cc_final: 0.7847 (tt) outliers start: 80 outliers final: 41 residues processed: 366 average time/residue: 1.5267 time to fit residues: 644.5991 Evaluate side-chains 350 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 149 optimal weight: 0.0570 chunk 211 optimal weight: 4.9990 chunk 39 optimal weight: 0.0030 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN O 44 ASN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105216 restraints weight = 36190.993| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.35 r_work: 0.3116 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 29124 Z= 0.144 Angle : 0.715 14.034 39862 Z= 0.274 Chirality : 0.039 0.364 3848 Planarity : 0.004 0.071 4636 Dihedral : 19.646 152.378 6926 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.18 % Allowed : 11.63 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2605 helix: 2.44 (0.12), residues: 1476 sheet: 0.35 (0.68), residues: 54 loop : -0.16 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.006 0.001 HIS W 29 PHE 0.019 0.001 PHE C 345 TYR 0.019 0.001 TYR L 164 ARG 0.007 0.000 ARG U 12 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 1338) hydrogen bonds : angle 4.14866 ( 3837) covalent geometry : bond 0.00334 (29065) covalent geometry : angle 0.71533 (39862) Misc. bond : bond 0.05637 ( 59) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 2.445 Fit side-chains REVERT: C 75 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: C 95 MET cc_start: 0.8691 (mmt) cc_final: 0.7515 (mmt) REVERT: C 131 MET cc_start: 0.8960 (mmt) cc_final: 0.8386 (mmt) REVERT: M 216 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8501 (t80) REVERT: I 1 MET cc_start: 0.6787 (mmt) cc_final: 0.6528 (mmt) REVERT: O 42 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7690 (tp40) REVERT: P 13 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7113 (mm-30) REVERT: P 17 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7433 (mt-10) REVERT: Q 41 VAL cc_start: 0.8850 (m) cc_final: 0.8543 (t) REVERT: T 14 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6593 (mt-10) REVERT: T 16 LYS cc_start: 0.8177 (mptt) cc_final: 0.7627 (mtpt) REVERT: U 11 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7251 (tmt170) REVERT: V 13 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6291 (mm-30) REVERT: V 23 MET cc_start: 0.8403 (mmm) cc_final: 0.8078 (mmm) REVERT: Y 3 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7575 (mtt90) REVERT: Z 11 SER cc_start: 0.7160 (p) cc_final: 0.6872 (p) REVERT: Z 17 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: 1 3 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7849 (mtt90) REVERT: 3 1 MET cc_start: 0.6715 (tpp) cc_final: 0.6247 (tpp) REVERT: 4 10 LEU cc_start: 0.7138 (mt) cc_final: 0.6933 (mp) REVERT: 4 13 GLU cc_start: 0.6826 (pp20) cc_final: 0.6506 (pp20) REVERT: 5 12 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6953 (ttt-90) REVERT: 5 36 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: 8 27 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7855 (tt) outliers start: 70 outliers final: 35 residues processed: 363 average time/residue: 1.5129 time to fit residues: 641.0758 Evaluate side-chains 347 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain S residue 4 MET Chi-restraints excluded: chain U residue 11 ARG Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 144 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 245 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102927 restraints weight = 36237.396| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.29 r_work: 0.3076 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.302 29124 Z= 0.207 Angle : 0.797 13.960 39862 Z= 0.310 Chirality : 0.042 0.359 3848 Planarity : 0.004 0.072 4636 Dihedral : 20.006 153.811 6920 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.36 % Allowed : 11.99 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2605 helix: 2.24 (0.12), residues: 1470 sheet: 0.41 (0.65), residues: 64 loop : -0.24 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.008 0.002 HIS W 29 PHE 0.025 0.002 PHE C 345 TYR 0.024 0.002 TYR L 164 ARG 0.007 0.001 ARG U 12 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 1338) hydrogen bonds : angle 4.27648 ( 3837) covalent geometry : bond 0.00493 (29065) covalent geometry : angle 0.79676 (39862) Misc. bond : bond 0.06410 ( 59) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 2.870 Fit side-chains REVERT: C 75 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6218 (mt-10) REVERT: C 309 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8265 (mtpt) REVERT: I 1 MET cc_start: 0.6775 (mmt) cc_final: 0.6554 (mmt) REVERT: J 9 ASN cc_start: 0.4884 (t0) cc_final: 0.4330 (t0) REVERT: J 17 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: O 42 GLN cc_start: 0.8315 (tt0) cc_final: 0.7768 (tp40) REVERT: P 17 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7426 (mt-10) REVERT: R 51 GLU cc_start: 0.8230 (pm20) cc_final: 0.8012 (pm20) REVERT: V 13 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6271 (mm-30) REVERT: V 23 MET cc_start: 0.8426 (mmm) cc_final: 0.8107 (mmm) REVERT: Y 3 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7597 (mtt90) REVERT: Z 11 SER cc_start: 0.7222 (p) cc_final: 0.6912 (p) REVERT: Z 17 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: 4 13 GLU cc_start: 0.6886 (pp20) cc_final: 0.6581 (pp20) REVERT: 5 36 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: 7 36 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: 8 27 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7905 (tt) outliers start: 74 outliers final: 41 residues processed: 352 average time/residue: 1.5166 time to fit residues: 615.9521 Evaluate side-chains 350 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 185 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101503 restraints weight = 36200.425| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.26 r_work: 0.3068 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.424 29124 Z= 0.259 Angle : 0.881 13.331 39862 Z= 0.342 Chirality : 0.045 0.345 3848 Planarity : 0.005 0.075 4636 Dihedral : 20.711 162.402 6920 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.27 % Allowed : 12.45 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2605 helix: 1.91 (0.12), residues: 1470 sheet: 0.32 (0.62), residues: 69 loop : -0.28 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 5 HIS 0.010 0.003 HIS W 29 PHE 0.029 0.002 PHE C 345 TYR 0.027 0.002 TYR L 164 ARG 0.010 0.001 ARG U 12 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 1338) hydrogen bonds : angle 4.43773 ( 3837) covalent geometry : bond 0.00620 (29065) covalent geometry : angle 0.88075 (39862) Misc. bond : bond 0.08224 ( 59) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 2.602 Fit side-chains REVERT: L 39 THR cc_start: 0.8709 (t) cc_final: 0.8458 (m) REVERT: J 9 ASN cc_start: 0.4982 (t0) cc_final: 0.4419 (t0) REVERT: J 17 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: J 30 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8517 (mp) REVERT: P 17 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7491 (mt-10) REVERT: S 6 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8200 (mtpm) REVERT: V 13 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6487 (mm-30) REVERT: V 23 MET cc_start: 0.8459 (mmm) cc_final: 0.8237 (mmm) REVERT: Y 3 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7607 (mtt90) REVERT: Z 11 SER cc_start: 0.7292 (p) cc_final: 0.7033 (p) REVERT: Z 17 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: Z 51 GLU cc_start: 0.7253 (pp20) cc_final: 0.7050 (pm20) REVERT: 4 10 LEU cc_start: 0.7244 (mt) cc_final: 0.7029 (mp) REVERT: 4 13 GLU cc_start: 0.6959 (pp20) cc_final: 0.6530 (pp20) REVERT: 5 36 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: 7 36 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: 8 27 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8066 (tp) outliers start: 72 outliers final: 40 residues processed: 365 average time/residue: 1.4845 time to fit residues: 626.0560 Evaluate side-chains 356 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103571 restraints weight = 36176.583| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.34 r_work: 0.3094 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.346 29124 Z= 0.172 Angle : 0.765 12.670 39862 Z= 0.295 Chirality : 0.040 0.336 3848 Planarity : 0.004 0.071 4636 Dihedral : 19.960 161.346 6917 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.82 % Allowed : 13.31 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.16), residues: 2605 helix: 2.19 (0.12), residues: 1469 sheet: 0.20 (0.65), residues: 59 loop : -0.22 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 PHE 0.021 0.002 PHE C 345 TYR 0.020 0.002 TYR L 164 ARG 0.006 0.000 ARG U 12 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 1338) hydrogen bonds : angle 4.27463 ( 3837) covalent geometry : bond 0.00405 (29065) covalent geometry : angle 0.76489 (39862) Misc. bond : bond 0.07069 ( 59) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 2.539 Fit side-chains REVERT: C 131 MET cc_start: 0.8983 (mmt) cc_final: 0.8403 (mmt) REVERT: H 87 ASP cc_start: 0.7736 (m-30) cc_final: 0.7462 (m-30) REVERT: P 17 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7485 (mt-10) REVERT: Q 41 VAL cc_start: 0.8844 (m) cc_final: 0.8539 (t) REVERT: S 6 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8197 (mtpm) REVERT: V 13 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6366 (mm-30) REVERT: V 23 MET cc_start: 0.8445 (mmm) cc_final: 0.8104 (mmm) REVERT: Y 3 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7589 (mtt90) REVERT: Z 11 SER cc_start: 0.7286 (p) cc_final: 0.7007 (p) REVERT: Z 17 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: 4 10 LEU cc_start: 0.7188 (mt) cc_final: 0.6979 (mp) REVERT: 4 13 GLU cc_start: 0.6904 (pp20) cc_final: 0.6609 (pp20) REVERT: 5 36 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: 7 36 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: 8 27 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (tp) REVERT: 9 42 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7925 (mt0) outliers start: 62 outliers final: 39 residues processed: 354 average time/residue: 1.5138 time to fit residues: 621.3495 Evaluate side-chains 353 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 9 residue 42 GLN Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 ASN H 172 GLN B 24 GLN G 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106176 restraints weight = 36156.247| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.35 r_work: 0.3140 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.308 29124 Z= 0.125 Angle : 0.698 12.168 39862 Z= 0.270 Chirality : 0.038 0.325 3848 Planarity : 0.004 0.070 4636 Dihedral : 18.849 159.773 6917 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.36 % Allowed : 14.04 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.16), residues: 2605 helix: 2.50 (0.12), residues: 1486 sheet: 0.16 (0.65), residues: 59 loop : -0.15 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 5 HIS 0.005 0.001 HIS M 301 PHE 0.019 0.001 PHE Q 18 TYR 0.019 0.001 TYR H 88 ARG 0.006 0.000 ARG W 12 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 1338) hydrogen bonds : angle 4.08630 ( 3837) covalent geometry : bond 0.00289 (29065) covalent geometry : angle 0.69849 (39862) Misc. bond : bond 0.05682 ( 59) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 2.649 Fit side-chains REVERT: C 95 MET cc_start: 0.8667 (mmt) cc_final: 0.7857 (mmt) REVERT: C 113 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6433 (p0) REVERT: C 131 MET cc_start: 0.8859 (mmt) cc_final: 0.8330 (mmt) REVERT: K 4 LEU cc_start: 0.8252 (tp) cc_final: 0.8001 (tm) REVERT: P 17 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7445 (mt-10) REVERT: Q 41 VAL cc_start: 0.8785 (m) cc_final: 0.8498 (t) REVERT: V 13 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6241 (mm-30) REVERT: V 23 MET cc_start: 0.8392 (mmm) cc_final: 0.8060 (mmm) REVERT: Y 3 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7634 (mtt90) REVERT: Z 11 SER cc_start: 0.7295 (p) cc_final: 0.7037 (p) REVERT: Z 14 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7230 (mt-10) REVERT: Z 17 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: 4 10 LEU cc_start: 0.7140 (mt) cc_final: 0.6939 (mp) REVERT: 4 13 GLU cc_start: 0.6873 (pp20) cc_final: 0.6535 (pp20) REVERT: 8 27 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7902 (tt) REVERT: 9 42 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7916 (mt0) outliers start: 52 outliers final: 26 residues processed: 361 average time/residue: 1.4969 time to fit residues: 626.0234 Evaluate side-chains 341 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 310 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 2 residue 12 ASP Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 9 residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 189 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN B 24 GLN G 24 GLN 4 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103936 restraints weight = 36024.945| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.32 r_work: 0.3102 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.330 29124 Z= 0.180 Angle : 0.777 11.849 39862 Z= 0.304 Chirality : 0.040 0.318 3848 Planarity : 0.004 0.072 4636 Dihedral : 19.176 161.691 6913 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.86 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.16), residues: 2605 helix: 2.34 (0.12), residues: 1483 sheet: 0.30 (0.68), residues: 54 loop : -0.21 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 252 HIS 0.008 0.002 HIS W 29 PHE 0.022 0.002 PHE H 21 TYR 0.023 0.002 TYR L 164 ARG 0.007 0.000 ARG W 12 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 1338) hydrogen bonds : angle 4.22201 ( 3837) covalent geometry : bond 0.00426 (29065) covalent geometry : angle 0.77722 (39862) Misc. bond : bond 0.06865 ( 59) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 2.565 Fit side-chains REVERT: C 95 MET cc_start: 0.8750 (mmt) cc_final: 0.7741 (mmt) REVERT: C 113 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6632 (p0) REVERT: M 236 GLU cc_start: 0.7806 (mp0) cc_final: 0.7605 (mm-30) REVERT: H 87 ASP cc_start: 0.7601 (m-30) cc_final: 0.7364 (m-30) REVERT: P 17 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7463 (mt-10) REVERT: Q 41 VAL cc_start: 0.8856 (m) cc_final: 0.8553 (t) REVERT: R 27 LEU cc_start: 0.7559 (mt) cc_final: 0.7127 (tp) REVERT: V 13 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6266 (mm-30) REVERT: V 23 MET cc_start: 0.8397 (mmm) cc_final: 0.8062 (mmm) REVERT: Y 3 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7644 (mtt90) REVERT: Z 17 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: 4 13 GLU cc_start: 0.6922 (pp20) cc_final: 0.6569 (pp20) REVERT: 5 36 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: 8 27 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7948 (tt) REVERT: 9 42 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7955 (mt0) outliers start: 41 outliers final: 28 residues processed: 347 average time/residue: 1.5197 time to fit residues: 615.4882 Evaluate side-chains 346 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 1 residue 9 ASP Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 9 residue 42 GLN Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 35 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 241 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN G 24 GLN 4 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103815 restraints weight = 36131.902| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.33 r_work: 0.3114 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 29124 Z= 0.155 Angle : 0.747 14.136 39862 Z= 0.290 Chirality : 0.039 0.318 3848 Planarity : 0.004 0.072 4636 Dihedral : 18.970 161.974 6913 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.91 % Allowed : 14.81 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.16), residues: 2605 helix: 2.38 (0.12), residues: 1483 sheet: 0.34 (0.68), residues: 54 loop : -0.19 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 5 HIS 0.007 0.002 HIS W 29 PHE 0.020 0.002 PHE H 21 TYR 0.020 0.001 TYR L 164 ARG 0.010 0.000 ARG U 12 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1338) hydrogen bonds : angle 4.18177 ( 3837) covalent geometry : bond 0.00363 (29065) covalent geometry : angle 0.74705 (39862) Misc. bond : bond 0.06547 ( 59) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20943.42 seconds wall clock time: 361 minutes 30.76 seconds (21690.76 seconds total)